spatialLayout           package:arrayMagic           R Documentation

_C_a_l_c_u_l_a_t_i_o_n _o_f _t_w_o _d_i_m_e_n_s_i_o_n_a_l _c_o_o_r_d_i_n_a_t_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     All 'value's are mapped on a matrix representing the the spatial
     layout defined by the function arguments, mainly by 'row',
     'column' and 'block' and 'numberOfValues' if not all values for
     all coordinates are given. The result can be  visualised with the
     function 'plot.imageMatrix'.

_U_s_a_g_e:

     spatialLayout(value, row, col, block, numberOfValues, nrOfBlocksPerRow = 4, mapping = 0)

_A_r_g_u_m_e_n_t_s:

   value: numeric vector; required; default: missing

     row: integer vector; required; default: missing

     col: integer vector; required; default: missing

   block: integer vector; required; default: missing

numberOfValues: integer; optional; default: missing. The argument
          'numberOfValues' allows to determine the correct spatial
          layout if not all values for all coordinates are passed to
          the function.

nrOfBlocksPerRow: integer; required; default: 4. Useful if there is a
          block structured layout with columns and rows assigned within
          each block as common for microarrays. See examples for a
          simple case with only one block.

 mapping: integer; either zero or one; default: zero, which corresponds
          to "ScanAlyze" and "GenePix"; cf. source code

_V_a_l_u_e:

     A matrix representing the spatial layout of all 'value's. The
     matrix is labelled as class 'imageMatrix' and 'matrix'.

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'plot.imageMatrix'

_E_x_a_m_p_l_e_s:

      value <- rep(c(1,rep(0,49)),10)
      block <- as.integer(gl(10,50))
      col <- rep(c(1:10),50)
      row <- rep(as.integer(gl(5,10)),10)
      sL <- spatialLayout(value=value,row=row,col=col,block=block,nrOfBlocksPerRow=2)
      plot.imageMatrix(sL)
      value <- value[-(201:250)]
      block <- block[-(201:250)]
      col <- col[-(201:250)]
      row <- row[-(201:250)]
      sL <- spatialLayout(value=value,row=row,col=col,block=block,nrOfBlocksPerRow=2,numberOfValues=500)
      plot.imageMatrix(sL)

      value <- 1:200
      block <- rep(1, 200)
      col <- rep(1:20, 10)
      row <- as.integer(gl(10,20))
      sLOne <- spatialLayout(value=value,block=block,col=col,row=row,nrOfBlocksPerRow=1)
             

